Simultaneous structural variation discovery in multiple paired-end sequenced genomes

Fereydoun Hormozdiari, Iman Hajirasouliha, Andrew McPherson, Evan E. Eichler, S. Cenk Sahinalp

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2 Citations (Scopus)

Abstract

Next generation sequencing technologies have been decreasing the costs and increasing the world-wide capacity for sequence production at an unprecedented rate, making the initiation of large scale projects aiming to sequence almost 2000 genomes [1]. Structural variation detection promises to be one of the key diagnostic tools for cancer and other diseases with genomic origin. In this paper, we study the problem of detecting structural variation events in two or more sequenced genomes through high throughput sequencing . We propose to move from the current model of (1) detecting genomic variations in single next generation sequenced (NGS) donor genomes independently, and (2) checking whether two or more donor genomes indeed agree or disagree on the variations (in this paper we name this framework Independent Structural Variation Discovery and Merging - ISV&M), to a new model in which we detect structural variation events among multiple genomes simultaneously.

Original languageEnglish (US)
Title of host publicationResearch in Computational Molecular Biology - 15th Annual International Conference, RECOMB 2011, Proceedings
PublisherSpringer-Verlag
Pages104-105
Number of pages2
ISBN (Print)9783642200359
DOIs
StatePublished - Jan 1 2011
Externally publishedYes

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume6577 LNBI
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Fingerprint

Genome
Genes
Sequencing
Genomics
Merging
High Throughput
Throughput
Diagnostics
Cancer
Costs
Model

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science(all)

Cite this

Hormozdiari, F., Hajirasouliha, I., McPherson, A., Eichler, E. E., & Sahinalp, S. C. (2011). Simultaneous structural variation discovery in multiple paired-end sequenced genomes. In Research in Computational Molecular Biology - 15th Annual International Conference, RECOMB 2011, Proceedings (pp. 104-105). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 6577 LNBI). Springer-Verlag. https://doi.org/10.1007/978-3-642-20036-6_11

Simultaneous structural variation discovery in multiple paired-end sequenced genomes. / Hormozdiari, Fereydoun; Hajirasouliha, Iman; McPherson, Andrew; Eichler, Evan E.; Sahinalp, S. Cenk.

Research in Computational Molecular Biology - 15th Annual International Conference, RECOMB 2011, Proceedings. Springer-Verlag, 2011. p. 104-105 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 6577 LNBI).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Hormozdiari, F, Hajirasouliha, I, McPherson, A, Eichler, EE & Sahinalp, SC 2011, Simultaneous structural variation discovery in multiple paired-end sequenced genomes. in Research in Computational Molecular Biology - 15th Annual International Conference, RECOMB 2011, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 6577 LNBI, Springer-Verlag, pp. 104-105. https://doi.org/10.1007/978-3-642-20036-6_11
Hormozdiari F, Hajirasouliha I, McPherson A, Eichler EE, Sahinalp SC. Simultaneous structural variation discovery in multiple paired-end sequenced genomes. In Research in Computational Molecular Biology - 15th Annual International Conference, RECOMB 2011, Proceedings. Springer-Verlag. 2011. p. 104-105. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). https://doi.org/10.1007/978-3-642-20036-6_11
Hormozdiari, Fereydoun ; Hajirasouliha, Iman ; McPherson, Andrew ; Eichler, Evan E. ; Sahinalp, S. Cenk. / Simultaneous structural variation discovery in multiple paired-end sequenced genomes. Research in Computational Molecular Biology - 15th Annual International Conference, RECOMB 2011, Proceedings. Springer-Verlag, 2011. pp. 104-105 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).
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